VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Sun Jul 20 2008 - 22:03:40 CDT

why not to select sth like
"same residue as protein and within 3 of water"
and make sure that the selection is updated every frame?
this would give you the water-exposed residues.

eddi

On Jul 20, 2008, at 4:28 PM, Christopher Gillespie wrote:

> Hello,
>
> I am trying to generate some rdfs for systems that I have already
> run. I want to do these using the protein surface as one
> selection. I know that using the selection "Protein and Surface"
> only implies "Not Buried" which removes hydrophobic residues from
> the selection set, but I want to see the actual atoms, including
> any hydrophobic ones that have at least some SASA, while also not
> including polar atoms that are actually buried, e.g. at the dimer
> interface. I know it may not be exactly correct since I should
> have to determine the SASA for each frame, but to make this doable
> in a reasonable amount of time and since my protein has an average
> RMSD of ~1.2A the atoms that make up the set from frame 0 should
> not deviate that much, I assume.
>
> So does anyone know how to define a selection of SASA > 0 atoms for
> use in gofr?
>
> Thanks
>
> Chris